Imo, titan abilities should be removed from the xp system and implemented in their own tech tree (like defence or diplomacy, except not). Hear me out here.
First, the four prototype technologies should be at levels 1-4 as is now. Then, when the fourth is researched, new research should become available: level 5 would have the first level of each ability, level 6 the second, level 7 the third, and level 8 would have fourth-level abilities as well as the ult. Researching the ult would be contingent on having a certain number of lower techs already researched, too. All of these researches should start off expensive and become progressively so. I wouldn’t consider 5k credits at all overkill for a level 4 ability or an ult, for example. Likewise, for abilities like level 1 snipe shot, we shouldn’t really be balking at paying ~2k credits. This will slow down titan construction immensely, which imo is a very good thing. We’ll end up seeing players be more willing to hunker down and entrench a broad economic base so that they can push out an upgraded titan.
Second, abilities should only be modifiable at the titan foundry. It should take, say, a two-minute cooldown to apply an ability to a titan, so that buffing your titan back up to its state upon death would take a lot of time, immobility (and possibly removal from your front line), but not a vast sum of credits (this would have been paid for when you initially researched the technology). (edit: I should add that a two-minute cooldown would be required for each level of an ability application. So upgrading your titan slowly but surely as you research the technologies would be viable, but if you lose your titan, it's going to be a long, long road getting it back up to speed again)
In doing this, building a titan foundry on your frontline would be incentivized, so that the titan could be re-buffed while still being a deterrent to invasions - but more importantly, your opponent would have a more viable method to counter your titan - destroying your frontline foundries. If you don't have a frontline foundry, well, fine - it'll be safe, but your titan will be kept out of the fight while it's being upgraded to its full strength again. In addition, this will incentivize the delaying of titan construction, again.
Thirdly, this allows for further titan-specific research to be conducted. Vasari/TEC/advent could have differing buffs to titan construction - reduced build time/reduced research time/faster upgrade application, for example.
Finally, titans should remain part of the xp system, even though they would no longer gain "ability points" - they'd still gain progressively larger amounts of hull, shield and antimatter, and more strike craft. In addition, what would be more reasonable than keeping 100% xp and levels would be level 2/3/4 titan technologies to keep 10/20/30% of the highest xp total achieved on previous titans - chalk that up to "lessons learned". Advent could either have these technologies at level 1/2/3, or instead receive 15/30/45% of previous xp. Edit 2: This really should have been a focal point of the post, in retrospect - I cannot stress enough how game-breaking it is that titans retain 100% of their experience (in addition to it being logic-defying outside of the Advent).